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[feat] added save_images for offline drift correction #3480

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[feat] added save_images for offline drift correction #3480

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23 changes: 21 additions & 2 deletions src/odemis/acq/drift/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,20 +20,24 @@
Odemis. If not, see http://www.gnu.org/licenses/.
"""

import datetime
import itertools
import logging
import math
import threading

import os
import numpy
import cv2

from odemis import model
from odemis.acq.align.shift import MeasureShift
from odemis.gui.util import get_picture_folder

MIN_RESOLUTION = (20, 20) # sometimes 8x8 works, but it's not reliable enough
MAX_PIXELS = 128 ** 2 # px

DRIFT_IMAGES_DIR = os.path.join(get_picture_folder(), "Drift Correction images")


class AnchoredEstimator(object):
"""
Expand All @@ -46,7 +50,7 @@ class AnchoredEstimator(object):
to measure the drift.
"""

def __init__(self, scanner, detector, region, dwell_time, max_pixels=MAX_PIXELS, follow_drift=True):
def __init__(self, scanner, detector, region, dwell_time, max_pixels=MAX_PIXELS, follow_drift=True, save_images=False):
"""
scanner (Emitter)
detector (Detector)
Expand All @@ -63,6 +67,12 @@ def __init__(self, scanner, detector, region, dwell_time, max_pixels=MAX_PIXELS,
self._semd = detector
self._dwell_time = dwell_time
self._follow_drift = follow_drift
self._save_images = save_images
self._session_id = datetime.datetime.now().strftime("%Y%m%d_%H%M%S")
self._image_counter = 0

if self._save_images:
os.makedirs(DRIFT_IMAGES_DIR, exist_ok=True)

# Latest drift vector from the previous acquisition
self.drift = (0, 0) # in sem px
Expand Down Expand Up @@ -143,6 +153,15 @@ def acquire(self):
if data.shape[::-1] != self._res:
logging.warning("Shape of data is %s instead of %s", data.shape[::-1], self._res)

# Save all the drift region scans for offline autocorrelation purposes
if self._save_images:
filename = os.path.join(DRIFT_IMAGES_DIR, f"drift_{self._session_id}_{self._image_counter:05d}.tif")
self._image_counter += 1

success = cv2.imwrite(filename, data)
if not success:
logging.warning("Failed to save drift image %s", filename)

# TODO: allow to record just every Nth image, and separately record the
# drift after every measurement
# In the mean time, we only save the 1st, 2nd and last two images
Expand Down
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